Align Mannitol-specific phosphotransferase enzyme IIA component, component of The mannitol porter (MtlA) (mannitol-1-P forming), MtlAF (characterized)
to candidate 17660 b3599 fused mannitol-specific PTS enzymes: IIA components/IIB components/IIC components (NCBI)
Query= TCDB::C0H3V2 (143 letters) >FitnessBrowser__Keio:17660 Length = 637 Score = 118 bits (296), Expect = 1e-31 Identities = 56/137 (40%), Positives = 89/137 (64%), Gaps = 2/137 (1%) Query: 4 LAKENIKLNQTVSSKEEAIKLAGQTLIDNGYVTEDYISKMFEREETSSTFMGNFIAIPHG 63 L ENI L + ++KEEAI+ AG+ L+ GYV +Y+ M +RE+ + T++G IA+PHG Sbjct: 496 LGAENIFLGRKAATKEEAIRFAGEQLVKGGYVEPEYVQAMLDREKLTPTYLGESIAVPHG 555 Query: 64 TEEAKSEVLHSGISIIQIPEGVEYG--EGNTAKVVFGIAGKNNEHLDILSNIAIICSEEE 121 T EAK VL +G+ Q PEGV +G E + A++V GIA +NNEH+ +++++ +E Sbjct: 556 TVEAKDRVLKTGVVFCQYPEGVRFGEEEDDIARLVIGIAARNNEHIQVITSLTNALDDES 615 Query: 122 NIERLISAKSEEDLIAI 138 IERL S ++++ + Sbjct: 616 VIERLAHTTSVDEVLEL 632 Lambda K H 0.310 0.130 0.342 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 179 Number of extensions: 6 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 143 Length of database: 637 Length adjustment: 26 Effective length of query: 117 Effective length of database: 611 Effective search space: 71487 Effective search space used: 71487 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.8 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory